finalRegions: finalRegions
In DEScan2: Differential Enrichment Scan 2

Description Usage Arguments Value Examples

Align peaks to form common regions then filter regions for presence in multiple replicates taking in input a GRangesList where each element is a sample of called peaks.

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finalRegions(peakSamplesGRangesList, zThreshold = 20, minCarriers = 2,
  saveFlag = TRUE, outputFolder = "overlappedPeaks", verbose = FALSE,
  scorecolname = "z-score", BPPARAM = BiocParallel::bpparam())

`peakSamplesGRangesList`	named GRangesList where each element is a sample of called peaks. A score mcols values is needed for each GRanges. The scorecolname param can be used as reference name for the score. (tipically returned by findPeaks function).
`zThreshold`	a minimum threshold for the z score. All peaks lesser than this value will be ignored.
`minCarriers`	a threshold of minimum samples (carriers) for overlapped regions.
`saveFlag`	a flag for saving results in a tsv file.
`outputFolder`	the directory name to store the bed file.
`verbose`	verbose output.
`scorecolname`	character describing the name of the column within the peaks score.
`BPPARAM`	object of class `bpparamClass` that specifies the back-end to be used for computations. See `bpparam` for details.

a GRanges of selected overlapping peaks with z-score, n-peaks, k-carriers as mcols object.

peak.path <- system.file("extdata/peaks/RData/peaksGRL_all_files.rds",
                            package="DEScan2")
grl <- readRDS(peak.path)
grl

regionsGR <- finalRegions(peakSamplesGRangesList=grl, zThreshold=1,
                        minCarriers=3, saveFlag=FALSE, verbose=TRUE)